## script to reclassify altitude output rasters to desired values and to create a flat lanscape
# plot rasters afterwards
rm(list = ls())
library(sp)
library(raster)
library(rgdal)
## rgdal: version: 1.5-10, (SVN revision 1006)
## Geospatial Data Abstraction Library extensions to R successfully loaded
## Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
## Path to GDAL shared files: /usr/share/gdal
## GDAL binary built with GEOS: TRUE
## Loaded PROJ runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
## Path to PROJ shared files: (autodetected)
## Linking to sp version:1.4-2
##### Create "flat" landscape #####
source("create_Flat.R")
create_Flat(inraster="../spatial/Elevation/NevTol_Alt.tif",
outname="../spatial/Elevation/NevTol_Alt_flat.asc")
## [1] "original raster"
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316384e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : /LUSTRE/Genetica/ngalvez/Multihierarchical_NevadoToluca/spatial/Elevation/NevTol_Alt.tif
## names : NevTol_Alt
##
## [1] "output raster"
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316244e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : NA
## source : /LUSTRE/Genetica/ngalvez/Multihierarchical_NevadoToluca/spatial/Elevation/NevTol_Alt_flat.asc
## names : NevTol_Alt_flat
##### Reclassify models #####
# so that non suitable habitat is set to NotS and suitable habitat to 1
source("reclass4circuit.R")
datafolder="../spatial/SDM/out"
##### Reclassify elevation models #####
# so that not suitable elevation is set to NotS and suitable to 1
# path to elevation raw data
datafolder="../spatial/Elevation"
# define in data and function
inraster=paste0(datafolder, "/NevTol_Alt.tif")
source("reclassElev4circuit.R")
## Do reclassification for several elevations
#for (i in c(2000, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700)) {
# print(paste("for min elevation:", i))
# outraster=paste0(datafolder, "/NevTol_Alt_", i, "_reclass.asc")
# # reclassify
# reclassElev4circuit(inraster, minElev=i, outraster, NotS=0.2)
# }
##### Raster Elevation Hipotesis "A"#########
myraster<-raster("../spatial/Elevation/NevTol_Alt.tif")
myraster
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316384e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : /LUSTRE/Genetica/ngalvez/Multihierarchical_NevadoToluca/spatial/Elevation/NevTol_Alt.tif
## names : NevTol_Alt
plot(myraster)
# read reclasification matrix (make sure no header)
# reclassify the values into three groups
rcl_Alt_A_reclass <- read.table("../spatial/Elevation/RasterAltitude_A.txt", sep = ",", header=F)
dim(rcl_Alt_A_reclass)
## [1] 9 3
class(rcl_Alt_A_reclass)
## [1] "data.frame"
rcl_Alt_A_reclass<- as.matrix(rcl_Alt_A_reclass)
class(rcl_Alt_A_reclass)
## [1] "matrix"
rcl_Alt_A_reclass
## V1 V2 V3
## [1,] 4000 4457 0.0
## [2,] 3386 4000 0.1
## [3,] 3189 3386 0.3
## [4,] 3164 3189 1.0
## [5,] 3139 3164 1.0
## [6,] 3010 3139 0.3
## [7,] 2600 3010 0.2
## [8,] 2000 2600 0.1
## [9,] 0 2000 0.0
# reclasify input raster
xa<-reclassify(myraster, rcl=rcl_Alt_A_reclass, include.lowest=FALSE, right=FALSE)
xa
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316384e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : NevTol_Alt
## values : 0, 1 (min, max)
plot(xa)
plot(xa, col=c("grey", "black"), legend=FALSE, xaxt='n', yaxt='n')
# save new raster
writeRaster(xa, filename="../spatial/Elevation/rcl_Alt_A.tif", format="GTiff", overwrite=TRUE)
writeRaster(xa, filename="../spatial/Elevation/rcl_Alt_A.asc", format="ascii", overwrite=TRUE)
###### Raster Altitude Hipotesis "B"############
# reclassify the values into three groups
rcl_Alt_B_reclass <- read.table("../spatial/Elevation/RasterAltitude_B.txt",sep = ",", header=F)
dim(rcl_Alt_B_reclass)
## [1] 8 3
class(rcl_Alt_B_reclass)
## [1] "data.frame"
rcl_Alt_B_reclass<- as.matrix(rcl_Alt_B_reclass)
class(rcl_Alt_B_reclass)
## [1] "matrix"
rcl_Alt_B_reclass
## V1 V2 V3
## [1,] 4000 4457 0.0
## [2,] 3386 4000 0.2
## [3,] 3189 3386 0.3
## [4,] 3164 3189 1.0
## [5,] 3139 3164 1.0
## [6,] 3010 3139 0.3
## [7,] 2000 3010 0.2
## [8,] 0 2000 0.0
# reclasify input raster
xb<-reclassify(myraster, rcl=rcl_Alt_B_reclass, include.lowest=FALSE, right=FALSE)
xb
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316384e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : NevTol_Alt
## values : 0, 1 (min, max)
plot(xb)
plot(xb, col=c("grey", "black"), legend=FALSE, xaxt='n', yaxt='n')
# save new raster
writeRaster(xb, filename="../spatial/Elevation/rcl_Alt_B.tif", format="GTiff", overwrite=TRUE)
writeRaster(xb, filename="../spatial/Elevation/rcl_Alt_B.asc", format="ascii", overwrite=TRUE)
##################SLOPE#############################
#Raster Slope Nevado de Toluca
myrasterS<-raster("../spatial/Slope/NevTol_Pen.tif")
myrasterS
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316384e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : /LUSTRE/Genetica/ngalvez/Multihierarchical_NevadoToluca/spatial/Slope/NevTol_Pen.tif
## names : NevTol_Pen
plot(myrasterS)
#######Raster Slope hipotesis "A"#####################
rcl_S_A <- read.table("../spatial/Slope/RasterValue_SlopeA.txt",sep = ",", header=F)
dim(rcl_S_A)
## [1] 3 3
class(rcl_S_A)
## [1] "data.frame"
rcl_S_A<- as.matrix(rcl_S_A)
class(rcl_S_A)
## [1] "matrix"
rcl_S_A
## V1 V2 V3
## [1,] 0.00 6.5700 1.0
## [2,] 6.57 13.1400 0.5
## [3,] 13.14 19.6999 0.2
# reclasify input raster Slope NT
x_SA<-reclassify(myrasterS, rcl=rcl_S_A, include.lowest=FALSE, right=FALSE)
x_SA
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316384e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : NevTol_Pen
## values : 0.2, 1 (min, max)
plot(x_SA)
# save new raster
writeRaster(x_SA, filename="../spatial/Slope/rcl_S_A.tif", format="GTiff", overwrite=TRUE)
writeRaster(x_SA, filename="../spatial/Slope/rcl_S_A.asc", format="ascii", overwrite=TRUE)
#############Raster Slope Hipotesis "B"###################
rcl_S_B <- read.table("../spatial/Slope/RasterValue_SlopeB.txt",sep = ",", header=F)
dim(rcl_S_B)
## [1] 3 3
class(rcl_S_B)
## [1] "data.frame"
rcl_S_A<- as.matrix(rcl_S_B)
class(rcl_S_B)
## [1] "data.frame"
rcl_S_B
## V1 V2 V3
## 1 0.00 6.5700 1.0
## 2 6.57 13.1400 0.7
## 3 13.14 19.6999 0.2
# reclasify input raster Slope NT
x_SB<-reclassify(myrasterS, rcl=rcl_S_B, include.lowest=FALSE, right=FALSE)
x_SB
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316384e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : NevTol_Pen
## values : 0.2, 1 (min, max)
plot(x_SB)
# save new raster
writeRaster(x_SB, filename="../spatial/Slope/rcl_S_B.tif", format="GTiff", overwrite=TRUE)
writeRaster(x_SB, filename="../spatial/Slope/rcl_S_B.asc", format="ascii", overwrite=TRUE)
#############Raster Slope Hipotesis "C"######################
rcl_S_C <- read.table("../spatial/Slope/RasterValue_SlopeC.txt",sep = ",", header=F)
dim(rcl_S_C)
## [1] 2 3
class(rcl_S_C)
## [1] "data.frame"
rcl_S_C<- as.matrix(rcl_S_C)
class(rcl_S_C)
## [1] "matrix"
rcl_S_C
## V1 V2 V3
## [1,] 0.00 6.5700 1.0
## [2,] 6.57 19.6999 0.2
# reclasify input raster Slope NT
x_SC<-reclassify(myrasterS, rcl=rcl_S_C, include.lowest=FALSE, right=FALSE)
x_SC
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316384e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : NevTol_Pen
## values : 0.2, 1 (min, max)
plot(x_SC)
# save new raster
writeRaster(x_SC, filename="../spatial/Slope/rcl_S_C.tif", format="GTiff", overwrite=TRUE)
writeRaster(x_SC, filename="../spatial/Slope/rcl_S_C.asc", format="ascii", overwrite=TRUE)
##############3Raster Slope Hipotesis "D"#######################
rcl_S_D <- read.table("../spatial/Slope/RasterValue_SlopeD.txt",sep = ",", header=F)
dim(rcl_S_D)
## [1] 2 3
class(rcl_S_D)
## [1] "data.frame"
rcl_S_C<- as.matrix(rcl_S_D)
class(rcl_S_D)
## [1] "data.frame"
rcl_S_D
## V1 V2 V3
## 1 0.0000 9.8499 1.0
## 2 9.8499 19.6999 0.2
# reclasify input raster Slope NT
x_SD<-reclassify(myrasterS, rcl=rcl_S_D, include.lowest=FALSE, right=FALSE)
x_SD
## class : RasterLayer
## dimensions : 3399, 3582, 12175218 (nrow, ncol, ncell)
## resolution : 9.316244e-05, 9.316384e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : NevTol_Pen
## values : 0.2, 1 (min, max)
plot(x_SD)
# save new raster
writeRaster(x_SD, filename="../spatial/Slope/rcl_S_D.tif", format="GTiff", overwrite=TRUE)
writeRaster(x_SD, filename="../spatial/Slope/rcl_S_D.asc", format="ascii", overwrite=TRUE)
######################################################################
###################Vegetation Type###############################
#Raster Vegetation Type in Nevado de Toluca
myrasterVT<-raster("../spatial/VegetationType/nevado_f.tif")
myrasterVT
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : /LUSTRE/Genetica/ngalvez/Multihierarchical_NevadoToluca/spatial/VegetationType/nevado_f.tif
## names : nevado_f
## values : 0, 255 (min, max)
plot(myrasterVT)
###########Vegetation Hipotesis "A"##########
#read reclasification matrix
rclA <- read.table("../spatial/VegetationType/RasterValue_A_G.txt",sep = ",", header=F)
dim(rclA)
## [1] 7 3
class(rclA)
## [1] "data.frame"
rclA<- as.matrix(rclA)
class(rclA)
## [1] "matrix"
rclA
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.1
## [5,] 3 4 0.7
## [6,] 2 3 1.0
## [7,] 1 2 1.0
# reclasify input raster
xVA<-reclassify(myrasterVT, rcl=rclA, include.lowest=FALSE, right=FALSE)
xVA
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVA)
# save new raster
writeRaster(xVA, filename="../spatial/VegetationType/rcl_A_G_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVA, filename="../spatial/VegetationType/rcl_A_G_3.asc", format="ascii", overwrite=TRUE)
###########Vegetation Hipotesis "B"##########
#read reclasification matrix
rclB <- read.table("../spatial/VegetationType/RasterValue_B_D.txt",sep = ",", header=F)
dim(rclB)
## [1] 7 3
class(rclB)
## [1] "data.frame"
rclB<- as.matrix(rclB)
class(rclB)
## [1] "matrix"
rclB
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.1
## [5,] 3 4 0.5
## [6,] 2 3 1.0
## [7,] 1 2 1.0
# reclasify input raster
xVB<-reclassify(myrasterVT, rcl=rclB, include.lowest=FALSE, right=FALSE)
xVB
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVB)
# save new raster
writeRaster(xVB, filename="../spatial/VegetationType/rcl_B_D_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVB, filename="../spatial/VegetationType/rcl_B_D_3.asc", format="ascii", overwrite=TRUE)
###########Vegetation Hipotesis "C"##########
#read reclasification matrix
rclC <- read.table("../spatial/VegetationType/RasterValue_C_C.txt",sep = ",", header=F)
dim(rclC)
## [1] 7 3
class(rclC)
## [1] "data.frame"
rclC<- as.matrix(rclC)
class(rclC)
## [1] "matrix"
rclC
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.1
## [5,] 3 4 0.2
## [6,] 2 3 1.0
## [7,] 1 2 1.0
# reclasify input raster
xVC<-reclassify(myrasterVT, rcl=rclC, include.lowest=FALSE, right=FALSE)
xVC
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVC)
# save new raster
writeRaster(xVC, filename="../spatial/VegetationType/rcl_C_C_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVC, filename="../spatial/VegetationType/rcl_C_C_3.asc", format="ascii", overwrite=TRUE)
###########Vegetation Hipotesis "D"##########
#read reclasification matrix
rclD <- read.table("../spatial/VegetationType/RasterValue_D_A.txt",sep = ",", header=F)
dim(rclD)
## [1] 7 3
class(rclD)
## [1] "data.frame"
rclD<- as.matrix(rclD)
class(rclD)
## [1] "matrix"
rclD
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.1
## [5,] 3 4 0.2
## [6,] 2 3 0.9
## [7,] 1 2 1.0
# reclasify input raster
xVD<-reclassify(myrasterVT, rcl=rclD, include.lowest=FALSE, right=FALSE)
xVD
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVD)
# save new raster
writeRaster(xVD, filename="../spatial/VegetationType/rcl_D_A_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVD, filename="../spatial/VegetationType/rcl_D_A_3.asc", format="ascii", overwrite=TRUE)
###########Vegetation Hipotesis "E"##########
#read reclasification matrix
rclE <- read.table("../spatial/VegetationType/RasterValue_E_B.txt",sep = ",", header=F)
dim(rclE)
## [1] 7 3
class(rclE)
## [1] "data.frame"
rclE<- as.matrix(rclE)
class(rclE)
## [1] "matrix"
rclE
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.1
## [5,] 3 4 0.2
## [6,] 2 3 0.7
## [7,] 1 2 1.0
# reclasify input raster
xVE<-reclassify(myrasterVT, rcl=rclE, include.lowest=FALSE, right=FALSE)
xVE
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVE)
# save new raster
writeRaster(xVE, filename="../spatial/VegetationType/rcl_E_B_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVE, filename="../spatial/VegetationType/rcl_E_B_3.asc", format="ascii", overwrite=TRUE)
###########Vegetation Hipotesis "F"##########
#read reclasification matrix
rclF <- read.table("../spatial/VegetationType/RasterValue_F_E.txt",sep = ",", header=F)
dim(rclF)
## [1] 7 3
class(rclF)
## [1] "data.frame"
rclF<- as.matrix(rclF)
class(rclF)
## [1] "matrix"
rclF
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.1
## [5,] 3 4 0.2
## [6,] 2 3 0.5
## [7,] 1 2 1.0
# reclasify input raster
xVF<-reclassify(myrasterVT, rcl=rclF, include.lowest=FALSE, right=FALSE)
xVF
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVF)
# save new raster
writeRaster(xVF, filename="../spatial/VegetationType/rcl_F_E_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVF, filename="../spatial/VegetationType/rcl_F_E_3.asc", format="ascii", overwrite=TRUE)
###########Vegetation Hipotesis "G"##########
#read reclasification matrix
rclG <- read.table("../spatial/VegetationType/RasterValue_G_F.txt",sep = ",", header=F)
dim(rclG)
## [1] 7 3
class(rclG)
## [1] "data.frame"
rclG<- as.matrix(rclG)
class(rclG)
## [1] "matrix"
rclG
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.1
## [5,] 3 4 0.2
## [6,] 2 3 0.2
## [7,] 1 2 1.0
# reclasify input raster
xVG<-reclassify(myrasterVT, rcl=rclG, include.lowest=FALSE, right=FALSE)
xVG
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVG)
# save new raster
writeRaster(xVG, filename="../spatial/VegetationType/rcl_G_F_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVG, filename="../spatial/VegetationType/rcl_G_F_3.asc", format="ascii", overwrite=TRUE)
###########Vegetation Hipotesis "H"##########
#read reclasification matrix
rclH <- read.table("../spatial/VegetationType/RasterValue_H_H.txt",sep = ",", header=F)
dim(rclH)
## [1] 7 3
class(rclH)
## [1] "data.frame"
rclH<- as.matrix(rclH)
class(rclH)
## [1] "matrix"
rclH
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.1
## [5,] 3 4 0.7
## [6,] 2 3 0.2
## [7,] 1 2 1.0
# reclasify input raster
xVH<-reclassify(myrasterVT, rcl=rclH, include.lowest=FALSE, right=FALSE)
xVH
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVH)
# save new raster
writeRaster(xVH, filename="../spatial/VegetationType/rcl_H_H_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVH, filename="../spatial/VegetationType/rcl_H_H_3.asc", format="ascii", overwrite=TRUE)
###########Vegetation Hipotesis "I"##########
#read reclasification matrix
rclI <- read.table("../spatial/VegetationType/RasterValue_I_I.txt",sep = ",", header=F)
dim(rclI)
## [1] 7 3
class(rclI)
## [1] "data.frame"
rclI<- as.matrix(rclI)
class(rclI)
## [1] "matrix"
rclI
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.2
## [5,] 3 4 0.2
## [6,] 2 3 0.2
## [7,] 1 2 1.0
# reclasify input raster
xVI<-reclassify(myrasterVT, rcl=rclI, include.lowest=FALSE, right=FALSE)
xVI
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVI)
# save new raster
writeRaster(xVI, filename="../spatial/VegetationType/rcl_I_I_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVI, filename="../spatial/VegetationType/rcl_I_I_3.asc", format="ascii", overwrite=TRUE)
###########Vegetation Hipotesis "J"##########
#read reclasification matrix
rclJ <- read.table("../spatial/VegetationType/RasterValue_J.txt",sep = ",", header=F)
dim(rclJ)
## [1] 7 3
class(rclJ)
## [1] "data.frame"
rclJ<- as.matrix(rclJ)
class(rclJ)
## [1] "matrix"
rclJ
## V1 V2 V3
## [1,] 7 8 0.0
## [2,] 6 7 0.0
## [3,] 5 6 0.1
## [4,] 4 5 0.5
## [5,] 3 4 0.7
## [6,] 2 3 1.0
## [7,] 1 2 1.0
# reclasify input raster
xVJ<-reclassify(myrasterVT, rcl=rclJ, include.lowest=FALSE, right=FALSE)
xVJ
## class : RasterLayer
## dimensions : 3400, 3583, 12182200 (nrow, ncol, ncell)
## resolution : 9.313644e-05, 9.313644e-05 (x, y)
## extent : -99.99505, -99.66134, 18.99265, 19.30931 (xmin, xmax, ymin, ymax)
## crs : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
## source : memory
## names : nevado_f
## values : 0, 1 (min, max)
plot(xVJ)
# save new raster
writeRaster(xVJ, filename="../spatial/VegetationType/rcl_I_I_3.tif", format="GTiff", overwrite=TRUE)
writeRaster(xVJ, filename="../spatial/VegetationType/rcl_I_I_3.asc", format="ascii", overwrite=TRUE)
##############################################